update

Author: sinamajidian

FastOMA/__init__.py

@@ -1,3 +1,3 @@
 
 __packagename__ = "FastOMA"
-__version__ = "0.1.1"
+__version__ = "0.1.2"

FastOMA/_config.py

@@ -39,7 +39,7 @@
 msa_write_all = False
 keep_subhog_each_pickle = False
 
-big_rhog_size = 80 * 1000
+big_rhog_size = 60 * 1000
 omamer_family_threshold = 110
 #
 # omamer_fscore_treshold_big_rhog = 0.04 # 0.5 # means no thresold #0.2 #0.5  #  to have more proteins in the ortho groups 0.05  considering for big rhogs
@@ -49,7 +49,7 @@
 # omamer_treshold_big_rhog_szie2 = 50*1000
 # omamer_fscore_treshold_big_rhog2 = 0.6 #0.9
 
-hogclass_max_num_seq = 50  # subsampling in msa # ver very 2
+hogclass_max_num_seq = 20  # subsampling in msa # ver very 2
 hogclass_min_cols_msa_to_filter = hogclass_max_num_seq * 50
 hogclass_tresh_ratio_gap_col = 0.6  # 0.8 for very very big
 # old code after samplign if there are 2 seq sampled, then at least one nongap
@@ -70,7 +70,7 @@
 rooting_mad_executable_path = "mad"  # /work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/installers/mad/
 
 ##inferhog
-inferhog_tresh_ratio_gap_row =0.1 # 0.6   # to have more proteins in the ortho groups 0.1
+inferhog_tresh_ratio_gap_row =0.4 # 0.6   # to have more proteins in the ortho groups 0.1
 inferhog_tresh_ratio_gap_col =0.5  # 0.6   # ver very 0.8
 inferhog_min_cols_msa_to_filter = 50 #300 #50  # used for msa before gene tree inference and  saving msa in hog class
 

README.md

@@ -265,6 +265,7 @@ HUMAN00034;HUMAN00035
 - phylostragraphy 
 
 ## Change log
+- Update  v0.1.2: improve rootHOG inference, splice 
 - Release  v0.1.0: improve nextflow pipeline and outputs. 
 - prelease v.0.0.6: use `--fragment-detection` for `infer-subhogs` and `--low-so-detection --fragment-detection`
 - prelease v.0.0.6: using input hogmpa